My shortstop is making a boatload of errors, way more than a big league shortstop should make. Why is that?

A.

It's all in the ratings and how he compares to the expected big league averages at the position.
The best place to compare a player with the expected big league average is on the Player Settings page in the Manager's Office. From there, click on the player's position link and the Position Assignment page will be opened. This page lists the expected fielding ratings for each position along with your player ratings. The more below average the player, the worse his fielding stats will be.